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Regional police spokesman Argo Yuwono said 103 workers were believed to be in the building at the time of the blast and that 10 remained unaccounted for, according to CNN Indonesia, a CNN affiliate.
"We don't know, however, if those 10 workers were actually in the factory at the time, or whether they may have been ill and not come to work," he said.
Thirty-four others were injured and have been taken to hospital, local police official Freddy Yudha said earlier.
Officials said that a large explosion took place, followed by a smaller one, and that a fire then broke out, leaving some of the victims with burns.
Images of the explosion show much of the factory's roof blown out and burned-out vehicles standing charred in the factory. Another showed a body in a bag being taken away.
Police are now working on identifying the bodies, Yuwono said.
The explosion occurred Thursday morning in Tangerang, a satellite city on Jakarta's western outskirts, where there are several industrial parks.
Ten fire trucks were sent to the scene, Muhammad Suhermanto, a local fire and disaster agency official, told CNN Indonesia.
He said that officials suspected an electrical short circuit caused a small fire and then triggered the explosion.
"There was a large explosion. Our suspicion is that the explosion was triggered by chemical materials inside the factory," Suhermanto said.
Indonesia has poor fire-safety standards and industrial fires are not uncommon. It is not the first time a deadly explosion has occurred at a fireworks factory in the country.